Kind of hard to advise without knowing the experiment, what questions you're trying to answer, or what you're trying to accomplish....have you read the literature? Papers such as Assessment of computational methods for the analysis of single-cell ATAC-seq data (Chen et al., 2019) or Comprehensive analysis of single cell ATAC-seq data with SnapATAC (Fang et al., 2021), and followed references in each? There's a ton of information to be had with a few hours of reading that might clear up a good number of week's confusion (hopefully?). Succinct explanations require some kind of foothold. Where are you stuck?

So I'm stuck after generating the .bed files. Don't know how to create a ChromatinAssay or some sort of object through that in order to generate peaks this way in Signac: https://stuartlab.org/signac/articles/peak_calling.html

After that, where do I proceed from here using the Signac pipeline? I'll take a look at the references, thanks!